All feature under manage.py command

[deming7h777]

For the ideal result of all the command for handle django database:

addorganism : python manage.py addorganism Aethina tumida

addblast : python manage.py addblast Aethina tumida -t peptide protein -f GCF_001937115.1_Atum_1.0_genomic.fna

makeblastdb : python manage.py blast_utility GCF_001937115.1_Atum_1.0_genomic.fna -m

populatesequence : python manage.py blast_utility GCF_001937115.1_Atum_1.0_genomic.fna -p

addhmmer : python manage.py addhmmer Aethina tumida -f GCF_001937115.1_Atum_1.0_genomic.fna

make blast is_shown:
python manage.py blast_shown GCF_001937115.1_Atum_1.0_genomic.fna --shown true/false
delete feature:
python manage.py delete -o Aethina tumida

python manage.py delete -b GCF_001937115.1_Atum_1.0_genomic.fna

python manage.py delete -h GCF_001937115.1_Atum_1.0_genomic.fna

[r06942072]

Checklist (I take organism honeybee as an example)

*addorganism

• python manage.py addorganism Apis mellifera

*addblast

• python manage.py addblast Apis mellifera -t peptide protein -f GCF_003254395.2_Amel_HAv3.1_genomic.fna

*makeblastdb

• python manage.py blast_utility GCF_003254395.2_Amel_HAv3.1_genomic.fna -m

*populatesequence

• python manage.py blast_utility GCF_003254395.2_Amel_HAv3.1_genomic.fna -p

*addhmmer

• python manage.py addhmmer Apis mellifera -f GCF_003254395.2_Amel_HAv3.1_genomic.fna

*delete

• python manage.py delete -o Apis mellifera

• python manage.py delete -b GCF_003254395.2_Amel_HAv3.1_genomic.fna

• python manage.py delete -h
  GCF_003254395.2_Amel_HAv3.1_genomic.fna

[r06942072]

merge branch addorg3 into master branch.
addorg3 add 5 more commands :

Checklist (I take organism honeybee as an example)

*addorganism

• python manage.py addorganism Apis mellifera

*addblast

• python manage.py addblast Apis mellifera -t peptide protein -f GCF_003254395.2_Amel_HAv3.1_genomic.fna

*makeblastdb

• python manage.py blast_utility GCF_003254395.2_Amel_HAv3.1_genomic.fna -m

*populatesequence

• python manage.py blast_utility GCF_003254395.2_Amel_HAv3.1_genomic.fna -p

*addhmmer

• python manage.py addhmmer Apis mellifera -f GCF_003254395.2_Amel_HAv3.1_genomic.fna

[mpoelchau]

Great!

• Documentation in readthedocs still needs to be updated
• function delete is in addorg2 - we'll need to set up a PR and test